I have been there with engine hosting and done alot of those steps
They had me enter a manual code into the database
But this still comes no where near any of issues
1. Have used the same code since september 2007 with no issue
2. have run it with a heck of a lot more traffic on my site with no issues
3. Problem started around when I was updated to the commercial version (around the same time)
4. Been having issues since around July-August 2010. Not every day, but in fits and starts.
5. But always around the same time of the day
this is part of my last note from engine hosting
I can get you access to the raw server logs if you would like.
This looks to be a problem with traffic. Please read this document http://ellislab.com/expressionengine/user-guide/general/handling_extreme_traffic.html
Especially note this section:
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Lastly, if you have a membership based site and have a sudden and tremendous influx of traffic of members who have not visited your site in a number of hours, the update of their last activity may cause a table lock. If you find this to be the case, you can have the server administrator run the following query after killing the locks, to delay the individual updates for members until a later time, perhaps when traffic is less tense. The example below pushes this off for another 20 hours (72000 seconds).
UPDATE exp_members SET last_activity = (UNIX_TIMESTAMP() + 72000)